ClinVar Miner

Variants from Provincial Medical Genetics Program of British Columbia, University of British Columbia with conflicting interpretations

Location: Canada  Primary collection method: clinical testing
Minimum review status of the submission from Provincial Medical Genetics Program of British Columbia, University of British Columbia: Collection method of the submission from Provincial Medical Genetics Program of British Columbia, University of British Columbia:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
91 27 1 18 1 0 4 21

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All submitters
Provincial Medical Genetics Program of British Columbia, University of British Columbia pathogenic likely pathogenic uncertain significance
pathogenic 1 11 3
likely pathogenic 7 0 0
benign 1 1 1

Submitter to submitter summary #

Total submitters: 26
Download table as spreadsheet
Submitter Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 2 0 4 0 0 2 6
Invitae 0 16 0 3 0 0 1 4
OMIM 0 20 0 3 0 0 0 3
Genomics England Pilot Project, Genomics England 0 1 0 3 0 0 0 3
Baylor Genetics 0 12 0 1 0 0 0 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 0 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 1 0 1 0 0 0 1
Mendelics 0 2 0 1 0 0 0 1
GeneReviews 0 6 1 0 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 3 0 1 0 0 0 1
LDLR-LOVD, British Heart Foundation 0 0 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 5 0 1 0 0 0 1
Center of Genomic medicine, Geneva, University Hospital of Geneva 0 1 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 0 0 0 0 0 1 1
Color Diagnostics, LLC DBA Color Health 0 1 0 1 0 0 0 1
Robarts Research Institute, Western University 0 0 0 1 0 0 0 1
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix 0 0 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 0 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 0 0 1 0 0 0 1
Fundacion Hipercolesterolemia Familiar 0 0 0 1 0 0 0 1
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital 0 0 0 1 0 0 0 1
SingHealth Duke-NUS Institute of Precision Medicine 0 1 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 0 1 0 1 1
Institute of Human Genetics, University Hospital Muenster 0 0 0 1 0 0 0 1
3billion 0 8 0 1 0 0 0 1
Payam Genetics Center, General Welfare Department of North Khorasan Province 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 21
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000035.4(ALDOB):c.448G>C (p.Ala150Pro) rs1800546 0.00319
NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn) rs6475 0.00117
NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser) rs113994152 0.00092
NM_004972.4(JAK2):c.1849G>T (p.Val617Phe) rs77375493 0.00036
NM_002834.5(PTPN11):c.794G>A (p.Arg265Gln) rs376607329 0.00003
NM_016042.4(EXOSC3):c.92G>C (p.Gly31Ala) rs387907196 0.00002
NM_000053.4(ATP7B):c.2621C>T (p.Ala874Val) rs121907994 0.00001
NM_000140.5(FECH):c.854A>G (p.Gln285Arg) rs370708663 0.00001
NM_000268.4(NF2):c.1193T>C (p.Leu398Pro) rs2147082680
NM_000500.9(CYP21A2):c.293-13C>G rs6467
NM_000527.5(LDLR):c.917C>T (p.Ser306Leu) rs11547917
NM_001110792.2(MECP2):c.352C>T (p.Arg118Trp) rs28934907
NM_001273.5(CHD4):c.3529C>T (p.Arg1177Cys) rs2136209186
NM_002016.2(FLG):c.2282_2285del (p.Ser761fs) rs558269137
NM_003482.4(KMT2D):c.5627_5630del (p.Asp1876fs) rs1555193738
NM_003590.5(CUL3):c.1549_1552del (p.Ser517fs) rs1692335353
NM_004380.3(CREBBP):c.4133G>C (p.Arg1378Pro) rs121434626
NM_021072.4(HCN1):c.835C>T (p.His279Tyr) rs587777495
NM_030777.4(SLC2A10):c.243C>G (p.Ser81Arg) rs80358230
NM_194454.3(KRIT1):c.1927C>T (p.Gln643Ter) rs1563240592
Single allele

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